Deck 19: Taking the Measure of Microbial Systems

Question 1

Amplification of chromosomal DNA from a single-cell is accomplished by

A) using PhyloChips.
B) using multiple displacement amplification.
C) creating complementary DNA from transcripts of a single-cell.
D) cloning fragments of the chromosome from the single-cell into a multi-copy plasmid.

Answer 1

B

Question 2

The term axenic is used to describe a(n)

A) anaerobic culture.
B) anoxygenic culture.
C) nutritionally deficient culture.
D) pure culture.

Answer 2

D

Question 3

In an agar dilution tube, microbial colonies grow

A) at the bottom of the tube.
B) on the sides of the tube, although some may be at the surface.
C) embedded in the agar, rather than growing on the surface.
D) on the surface, but some creep down the sides away from the surface.

Answer 3

C

Question 4

Laser tweezers are most directly used for

A) enriching a culture.
B) isolating individual cells.
C) increasing magnification.
D) enhancing the growth of fastidious organisms.

Question 5

The methodology of microbial ecology includes

A) enrichment and isolation of specific microbes.
B) cell-staining methods.
C) gene, transcript, and protein characterization.
D) enrichment and isolation of specific microbes, cell-staining, and characterization of genes, transcripts, and proteins.

Question 6

Phylogenetic stains, such as those used in phylogenetic FISH, hybridize with

A) ribosomal RNA.
B) mitochondrial DNA.
C) nuclear DNA.
D) RNA polymerase.

Question 7

Which fluorescent molecule enables visualization of living microorganisms?

A) acridine orange
B) DAPI
C) GFP
D) SYBR Green

Question 8

What technique(s) can be used to characterize the phylogenetic composition of a microbial community without culturing any of the members?

A) green fluorescent protein tagging
B) stable isotope techniques
C) radioisotope experiments
D) fluorescent in situ hybridization (FISH)

Question 9

Which approach would help to identify biologically produced sulfur in a sediment sample?

A) enrichment
B) isotopic fractionation
C) microautoradiography
D) microelectrodes

Question 10

For microbial biodiversity studies, it is common to identify the ________ rather than the ________ as a measure of biodiversity.

A) organisms themselves / genes
B) genes / organisms themselves
C) cell types / genes
D) cell types / organisms themselves

Question 11

The biggest limitation of traditional light microscopy and electron microscopy is that they are unable to reveal

A) absolute cell concentration.
B) cellular components of small microbes because of the limits of magnification.
C) functional diversity of microorganisms in the habitat under study.
D) physical microbial interactions as found in nature.

Question 12

Staining methods are suitable for obtaining

A) information about physiology from natural samples.
B) quantitative information from natural samples.
C) phylogenetic information from natural samples.
D) neither qualitative nor quantitative information from natural samples.

Question 13

Which method requires the addition of at least one radioactive chemical?

A) CARD-FISH
B) MAR
C) GeoChips
D) SIP

Question 14

Which of the following methods do NOT involve nucleic acid hybridization of a probe to a specimen?

A) RACE-FISH
B) FISH-MAR
C) PhyloChips
D) T-RFLP

Question 15

When dealing with stable isotopes of carbon and sulfur, enzymes tend to favor

A) the lighter isotope.
B) the heavier isotope.
C) the isotopes in about equal proportions.
D) either the lighter or the heavier isotope, depending on environmental conditions.

Question 16

The science of microbial ecology deals with

A) how microbial communities interact with each other and their environment.
B) microbial activity and biodiversity.
C) microbial gene regulation mechanisms in response to environmental change.
D) how the activity and biodiversity of microbial communities affect microbial interactions with each other and the environment.

Question 17

Well-designed microbial activity measurements can reveal ________ of major metabolic reactions in a habitat.

A) types
B) rates
C) both types and rates
D) either types or rates (but not both)

Question 18

Radioisotopes are useful when

A) very high sensitivity is required.
B) turnover rates need to be determined.
C) the fate of portions of particular molecules need to be followed.
D) very high sensitivity is required, turnover rates need to be determined, and the fate of portions of particular molecules need to be followed.

Question 19

The term used when an organism is studied in its natural environment is

A) au naturale.
B) in vitro.
C) in situ.
D) in toto.

Question 20

Winogradsky columns are used primarily for enrichment of

A) aerobic cultures, although occasionally anaerobes do appear.
B) anaerobic cultures, although occasionally aerobes do appear.
C) aerobes, anaerobes, and phototrophs.
D) phototrophs, although occasionally heterotrophs do appear.

Question 21

When laser tweezers are used, the laser beam can trap

A) an isolated single-copy genome in a capillary tube.
B) a single microbial cell in a capillary tube.
C) a single microbial colony on a plate.
D) multiple cells of the same type on a plate.

Question 22

What unit is isotopic fractionation reported as?

A) parts per billion
B) parts per hundred
C) parts per thousand
D) parts per trillion

Question 23

Genes encoding ________ are widely used as target genes in molecular biodiversity studies.

A) ATPases
B) DNA polymerase III
C) 16S rRNA
D) RNA polymerase

Question 24

How do viability stains usually distinguish between living cells and dead cells?

A) The chemical fluoresces only when bound to ribosomes that are actively synthesizing proteins.
B) The chemical stain is taken up by living cells and once metabolized becomes fluorescent.
C) The dye specifically targets intact cytoplasmic membranes.
D) The dyeʹs fluorescence is quenched by dead cells.

Question 25

Thirty organisms containing the same phylogenetic marker, with identical or similar orthologous genes, are all considered to be within the same

A) phylotype.
B) species.
C) functional group.
D) phylogenetic tree.

Question 26

Microarrays are useful for assessing

A) gene expression only.
B) enzyme activity.
C) the presence of specific rRNA sequences only.
D) gene expression and the presence of specific rRNA sequences.

Question 27

Which of the following techniques can link prokaryotic phylogeny and metabolic function?

A) DAPI staining
B) stable isotope probing only
C) environmental genomics only
D) environmental genomics and stable isotope probing

Question 28

Which technique would be used to estimate the concentration of naturally occurring Escherichia coli in a wastewater sample?

A) agar dilution tube method
B) laser tweezers method
C) most probable number (MPN) method
D) cell tagging using GFP method

Question 29

Pure cultures can be obtained from an enrichment culture using

A) streak plates only.
B) the agar dilution method only.
C) liquid dilution methods only.
D) streak plates, the agar dilution method, or liquid dilution methods.

Question 30

Metatranscriptomics and metaproteomics are favored over metagenomics when ________ is of more interest than ________.

A) gene presence / phylogeny
B) phylogeny / gene presence
C) function or gene expression / gene presence
D) gene presence / function or gene expression

Question 31

Analyses of sulfur isotopes have been used as evidence against life on the Moon, because the sulfides in lunar rocks have

A) an isotope composition most similar to marine sulfate, which is enriched in ³⁴S.
B) an isotope composition most similar to marine mud, which is enriched in ³⁴S.
C) an isotope composition most similar to igneous rocks.
D) exactly equal amounts of ³⁴S and ³²S.

Question 32

For what purpose would a microbial ecologist use a microsensor?

A) to determine the concentration of cells in small increments in a sediment or water column
B) to determine the expression of a particular gene in a microbial community
C) to quantify the uptake of a radioactive material
D) to determine the concentration of O₂, N₂O, or other chemical species in small increments in a sediment or water column

Question 33

In microbial ecology studies, the FISH technique identifies organisms based on

A) the presence of green fluorescent protein.
B) fluorescence of unique cofactors or pigments under certain wavelengths of UV light.
C) hybridization of a fluorescent probe to specific ribosomal RNA sequences.
D) the presence of luciferase.

Question 34

Why is it necessary to have a standard for the interpretation of stable isotope ratios?

A) A standard is necessary to calculate how rapidly the stable isotopes undergo radioactive decay.
B) A standard is necessary to determine the stable isotope ratio in the absence of biological activity.
C) A standard is necessary because samples are only presented in comparison with other samples of the same age.
D) A standard is necessary to determine the age of the sample.

Question 35

Which molecular method allows for the detection of a specific organism within a diverse microbial community?

A) fluorescent DNA staining using DAPI
B) viability staining
C) enrichment techniques
D) fluorescent in situ hybridization (FISH)

Question 36

What are activity measurements?

A) Activity measurements are any measurements taken in vitro.
B) Activity measurements are any measurements taken in situ.
C) Activity measurements are collective estimates of the physiological reactions in an entire microbial community.
D) Activity measurements are an example of metagenomics, which can be used when genetic analysis is difficult.

Question 37

Diversity is often ________ when T-RFLP is used.

A) underestimated
B) overestimated
C) randomly overestimated or underestimated
D) impossible to estimate

Question 38

Robotic systems used to quickly test the response of microbes in microtiter plates to thousands of combinations of nutrients is an example of a(n) ________ technology.

A) next generation sequencing
B) stable isotope
C) genomic
D) high-throughput

Question 39

Genomic analysis of Prochlorococcus has revealed

A) the presence of bacteriorhodopsin.
B) that no regions are shared between cultured representatives and environmental populations.
C) complete congruence of genes and genome structure within the same phylotype.
D) high levels of gene conservation between cultured representatives and environmental populations.

Question 40

Interpreting stable isotopic fractionation depends on the fact that most enzymes preferentially bind ________ isotope substrates over ________ isotope substrates.

A) nonradioactive / radioactive
B) light / heavy
C) heavy / light
D) radioactive / nonradioactive

Question 41

The overall purpose of DGGE is to

A) separate genes that differ in length.
B) measure the activity of cells that use DGGE as an energy source.
C) detect cells that utilize a specific radiolabeled substrate.
D) separate genes of the same length that have different sequences, resulting in different denaturation profiles.

Question 42

Single-cell genomics may help us

A) predict which microbes will be abundant based on the environmental conditions.
B) understand the physiology of uncultured microbes.
C) develop better enrichment culture methods.
D) understand the physiology of uncultured microbes and develop better enrichment culture methods.

Question 43

Strict anaerobic organisms are not suited for GFP reporters due to the protein requiring oxygen to fluoresce.

Question 44

The ¹³C/¹²C isotopic ratio of geological rocks of different ages has been used to examine whether previous biological activity occurred because compounds of biological origin

A) do NOT contain ¹³C.
B) have a higher proportion of ¹³C that compounds of geological origin.
C) have a lower proportion of ¹³C that compounds of geological origin.
D) are not well preserved in geological samples.

Question 45

If properly constructed, a Winogradsky column can be used to isolate pure cultures.

Question 46

Once a putative pure culture has been obtained from the environment, it is no longer necessary to check its purity.

Question 47

Stable isotope probing (SIP) is a method that

A) causes cells that hybridize with a fluorescent probe to fluoresce under UV light.
B) compares the isotopic ratios of different compounds in the environment to determine whether they are of biological or geological origin.
C) uses substrates containing heavy isotopes to label the DNA of organisms that use those substrates.
D) compares the transcription of specific isotope labeled genes under different conditions.

Question 48

Transcription of various genes under particular environmental conditions in natural populations can be studied using

A) CARD-FISH.
B) stable isotope analysis.
C) T-RFLP.
D) green fluorescent protein (GFP).

Question 49

The goal of environmental genomics is to detect as many genes as possible and then, if possible, to determine to the phylogeny of the organisms to which the genes belong.

Question 50

You would like to test the hypothesis that ammonia-oxidizing Archaea are more active and abundant than ammonia-oxidizing Bacteria in coastal marine water. What technique(s) or experiment(s) could you use to test this hypothesis?

A) environmental proteomics
B) fluorescent in situ hybridization (FISH)
C) stable isotope probing using ¹⁵N labeled ammonia
D) stable isotope ratios of ammonia and nitrite

Question 51

Enrichment cultures can be established by placing the inoculum into selective media and incubating under specific conditions.

Question 52

Culture-independent approaches avoid issues associated with

A) detecting very rare phylotypes.
B) conflating phylogenetic and functional diversity.
C) growing organisms in the lab.
D) next generation sequencing.

Question 53

The purpose of the enrichment culture technique is to enrich for organisms with specific physiological properties from a microbial community.

Question 54

One way to study a microbial ecosystem is to isolate microorganisms from it and study their properties in laboratory culture.

Question 55

Organisms in natural environments can be detected by assaying for the presence of their genes.

Question 56

Traditional enrichment culturing circumvents issues associated with ʺweedʺ species from overcoming the population.

Question 57

The element(s) that have proven most useful for stable isotope studies are

A) carbon only.
B) nitrogen only.
C) sulfur only.
D) carbon, sulfur, and sometimes nitrogen.

Question 58

Which of the following hypotheses could be tested using microautoradiography fluorescence in situ hybridization (MAR-FISH)?

A) Bacteriorodopsin uses light energy to translocate protons.
B) Archaea are the main autotrophs in marine water samples taken 300 m below the surface of the ocean.
C) The microbial community of agricultural soils is more phylogenetically diverse than the microbial community of native prairie soils.
D) The ammonia monooxygenase gene is present in members of the phylum Verrucomicrobium.

Question 59

Which of the following statements is FALSE concerning enrichment bias?

A) Dilution of the inoculum may help to avoid enrichment bias in some cases.
B) Enrichment bias is impossible to overcome in some oligotrophic environments.
C) Enrichment bias resulted in the underestimation of prokaryotic diversity.
D) Enrichment bias favors organisms that grow quickly.

Question 60

How would you label and separate the DNA of unknown methylotrophs in a sample?

A) Incubate the sample with ¹³C-methane.
B) Hybridize the DNA to FISH probes.
C) Use DGGE to separate the strands of DNA in the sample.
D) Use T-RFLP to identify the methylotroph DNA in the sample.

Question 61

In natural samples it is often difficult to differentiate live cells from dead cells or cells from nonliving matter without special dyes.

Question 62

The diversity of microorganisms in culture collections is representative of the diversity of microorganisms found in nature.

Question 63

What are the pros and cons of traditional enrichment culture techniques? What advances in the last decade are improving enrichment culture techniques to aid the cultivation of uncultured microorganisms?

Question 64

Describe how FISH can be used to determine which cells within a microbial community are actively degrading toluene. Assume the genes involved in the metabolic pathway have been sequenced from several microorganisms and vary only slightly from one another.

Question 65

Metaproteomics is a more developed field than metatranscriptomics due to the high sensitivity of mass spectrometry.

Question 66

DGGE and T-RFLP are both molecular microbial ecology methods that use polymerase chain reaction (PCR) to amplify specific genes to assess diversity.

Question 67

Describe what an ITS region is in the context of prokaryotes, and explain the significance of the ITS region for microbial ecology.

Question 68

A study of the human gut performed in 1982 used various types of plates under different growth conditions to describe and enumerate the microbes in the human gut. They concluded that the majority of the microbes in the human gut are Gammaproteobacteria. A study conducted in 2010 using next-generation sequencing to characterize 16S rRNA sequences concluded that the majority of the microbes in the human gut are Firmicutes and Bacteriodetes. Why did these studies have different conclusions? Which study do you think is most accurate?

Question 69

The Winogradsky column is a method for assessing the entire gene complement of a habitat, revealing both the biodiversity and metabolic capabilities of the microbial community at the same time.

Question 70

Propose an experiment to identify members capable of assimilating monomers of lignin within a microbial community.

Question 71

Fluorogenic dyes, autofluorescence, and genetically engineered autofluorescence can be used to identify cells.

Question 72

Using specific examples, when is it appropriate to use CARD-FISH rather than the traditional FISH method and vice-versa?

Question 73

What prior knowledge is required to use a phylochip to study the abundance of the different microbes present within a microbial community? How does this cause bias when using a phylochip to analyze microbial community structure?

Question 74

Combined with autofluoresence or fluorescent DNA probes, flow cytometry can separate or count populations of cells from aquatic environments.

Question 75

The MPN technique is rarely applied in the food industry because any microbial presence in food is unsafe.

Question 76

We know that that there are over 50 major phyla in Bacteria; however, only about 25 of these phyla have cultured representatives. Why is this? How are scientists attempting to culture representative from the 25 phyla that do not currently have any organisms in culture?

Question 77

By using simple microscopy techniques, it is possible to determine if a pure culture is contaminated with another organism.

Question 78

Phototrophic organisms in SIP experiments are often observed releasing ¹⁴CO₂ as a way of measuring photosynthetic activity.

Question 79

How can NanoSIMS be used to determine which Roseobacters most strongly use DMSP as a sulfur source within a coastal marine environment? Explain the NanoSIMS methodology in your answer.

Question 80

FISH technology can employ only a single phylogenetic probe.